Difference between revisions of "Molecular Dynamics Simulations Hemochromatosis"
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| − | == |
+ | == Riddle of the task == |
| + | Sorry, not this week. Too busy... |
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| − | Detailed description: [[Task_8_-_Molecular_Dynamics_Simulations|Molecular dynamics simulations]] |
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| + | Meanwhile you could go on a journey or quest: [http://www.journey-quest.com/ Journey Quest] |
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| − | == |
+ | == Short task description == |
| + | Detailed description: [[Task_8_-_Molecular_Dynamics_Simulations|Molecular dynamics simulations]] |
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| − | A protocol with a description of the data acquisition and other scripts used for this task is available [[Task8 Hemochromatosis Protocol|here]]. |
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| − | == |
+ | == Protocol == |
| + | A protocol with a description of the data acquisition and other scripts used for this task is available [[Task8 Hemochromatosis Protocol|here]]. |
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| − | Coming soon... |
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Starting mutation runs: |
Starting mutation runs: |
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| − | * Wildtype (status: pending) |
+ | * Wildtype (status: still pending...) |
| − | * R224W (status: pending) |
+ | * R224W (status: still pending...) |
| − | * C282S (status: pending) |
+ | * C282S (status: still pending...) |
| + | |||
| + | ...approximated start: Sunday or Monday -.- |
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Revision as of 11:08, 30 June 2012
Hemochromatosis>>Task 8: Molecular dynamics simulations
Contents
Riddle of the task
Sorry, not this week. Too busy... Meanwhile you could go on a journey or quest: Journey Quest
Short task description
Detailed description: Molecular dynamics simulations
Protocol
A protocol with a description of the data acquisition and other scripts used for this task is available here.
Diary of "trial and error"-hell...
Tipps for other groups:
- AGroS wants to run "scwrl" and not "Scwrl4" which is the name after the installation.
- Solution: ln -s Scwrl4 scwrl
- Problems NVT!!! (Can not open file: *_nvt.tpr).
- Solution: reduce to 16 cores (instead of 32)
- Anybody tried 32 cores on the real runs??
- Yes, tried and it worked in the real run. The --partition=inter queue still throws segfaults on the NVT run, though.. ;)
- Anybody tried 32 cores on the real runs??
- Solution: reduce to 16 cores (instead of 32)
Current "test" state:
- Run min I: solvent & fixed protein(SD) ...finished
- Run min II: solvent & fixed backbone(SD) ...finished
- Run min III: solvent & fixed backbone(CG) ...finished
- Run NVT ...finished
- Run NPT ...finished
- Production run ...terminated after the 2 hour limit (without errors)
Starting mutation runs:
- Wildtype (status: still pending...)
- R224W (status: still pending...)
- C282S (status: still pending...)
...approximated start: Sunday or Monday -.-
